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Question: Bioconductor: quantile normalization
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gravatar for KVC_bioinfo
12 weeks ago by
KVC_bioinfo0 wrote:

Hello All,

I have used Bioconductor ‘preprocessCore’ fro quantile normalization. I am trying t understand how does it work with low expressed or zero count genes. Is someone aware of that? Does it remove the low expressed genes?

TIA

 

 

ADD COMMENTlink modified 12 weeks ago by James W. MacDonald46k • written 12 weeks ago by KVC_bioinfo0
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gravatar for James W. MacDonald
12 weeks ago by
United States
James W. MacDonald46k wrote:

No, it doesn't remove anything. It wouldn't make any sense to do that. If you look at the help page for normalize.quantiles, there is a link to a pdf that explains the procedure.

That said, preprocessCore, and normalize.quantiles are intended for microarray measurements, and using for count data is probably suboptimal.

ADD COMMENTlink written 12 weeks ago by James W. MacDonald46k

Thank you very much. I have used that on RNA-seq counts 

ADD REPLYlink written 12 weeks ago by KVC_bioinfo0

Well, like I said, that is probably not what you want to do. There are established RNA-Seq analysis pipelines, such as DESeq2 and edgeR, which handle the normalization of the count data in a statistically defensible manner. Unless you know what you are doing, it's probably best to use existing tools rather than a hodgepodge of methods borrowed from various analysis pipelines.

ADD REPLYlink written 12 weeks ago by James W. MacDonald46k
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